Bio::PopGen::Individual - An implementation of an Individual who has Genotype or Sequence Results
use Bio::PopGen::Individual; my $ind = Bio::PopGen::Individual->new(-unique_id => $id, -genotypes => \@genotypes);
This object is a container for genotypes.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = Bio::PopGen::Individual->new(); Function: Builds a new Bio::PopGen::Individual object Returns : an instance of Bio::PopGen::Individual Args : -unique_id => $id, -genotypes => \@genotypes
Title : unique_id Usage : my $id = $individual->unique_id Function: Unique Identifier Returns : string representing unique identifier Args : string
Title : num_of_results Usage : my $count = $person->num_results; Function: returns the count of the number of Results for a person Returns : integer Args : none
Title : annotation Usage : my $annotation_collection = $ind->annotation; Function: Get/set a Bio::AnnotationCollectionI for this individual Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object
Title : add_Genotype Usage : $individual->add_Genotype Function: add a genotype value Returns : count of the number of genotypes associated with this individual Args : @genotypes - L<Bio::PopGen::GenotypeI> object(s) containing alleles plus a marker name
Title : reset_Genotypes Usage : $individual->reset_Genotypes; Function: Reset the genotypes stored for this individual Returns : none Args : none
Title : remove_Genotype Usage : $individual->remove_Genotype(@names) Function: Removes the genotypes for the requested markers Returns : none Args : Names of markers
Title : get_Genotypes Usage : my @genotypes = $ind->get_Genotypes(-marker => $markername); Function: Get the genotypes for an individual, based on a criteria Returns : Array of genotypes Args : either none (return all genotypes) or -marker => name of marker to return (exact match, case matters)
Title : has_Marker Usage : if( $ind->has_Marker($name) ) {} Function: Boolean test to see if an Individual has a genotype for a specific marker Returns : Boolean (true or false) Args : String representing a marker name
Title : get_marker_names Usage : my @names = $individual->get_marker_names; Function: Returns the list of known marker names Returns : List of strings Args : none
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.